Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
vidjil
vidjil
Commits
880abf7d
Commit
880abf7d
authored
Sep 13, 2017
by
Mathieu Giraud
Browse files
should-get-tests/*.should-get: replace $VIDJIL_DIR/data by $VIDJIL_DATA
See
#2611
.
parent
35525c10
Changes
70
Hide whitespace changes
Inline
Side-by-side
algo/tests/should-get-tests/10-md5-data.should-get
View file @
880abf7d
!NO_LAUNCHER:
!LAUNCH: (cd $VIDJIL_D
IR/data
; md5sum *.fasta || md5 -r *.fasta)
!LAUNCH: (cd $VIDJIL_D
ATA
; md5sum *.fasta || md5 -r *.fasta)
$ Check md5 in data/
1:985219d9156b6d9e8966807595beada3 Stanford_S22.fa
...
...
algo/tests/should-get-tests/ambiguous_representative.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -k 4 -w 20 -z 0 -c clones -V $VIDJIL_D
IR/data
/toy_V.fa -J $VIDJIL_D
IR/data
/toy_J.fa $VIDJIL_D
IR/data
/ambiguous_representative.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -k 4 -w 20 -z 0 -c clones -V $VIDJIL_D
ATA
/toy_V.fa -J $VIDJIL_D
ATA
/toy_J.fa $VIDJIL_D
ATA
/ambiguous_representative.fa
$ Short reads properly segmented
1:SEG_+.* -> .* 4
...
...
algo/tests/should-get-tests/ambiguous_representative2.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -c clones -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
IR/data
/test_representatives.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -c clones -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_D
ATA
/test_representatives.fa
$ Three clones should be found
1:3 clones
...
...
algo/tests/should-get-tests/cdr3-stopcodon.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_D
IR/data
/cdr3-stopcodon.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_D
ATA
/cdr3-stopcodon.fa
!LOG: out/cdr3-stopcodon.vidjil
$ Two identical junctions in JSON
...
...
algo/tests/should-get-tests/cgi-align.should-get
View file @
880abf7d
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_D
IR/data
/msa.fa
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_D
ATA
/msa.fa
$ no spurious info
0: .* bp in .* sequences
...
...
algo/tests/should-get-tests/cgi-align2.should-get
View file @
880abf7d
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_D
IR/data
/msa2.fa
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_D
ATA
/msa2.fa
$ no spurious info
0: .* bp in .* sequences
...
...
algo/tests/should-get-tests/cgi-align3.should-get
View file @
880abf7d
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_D
IR/data
/msa3.fa
!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_D
ATA
/msa3.fa
$ no spurious info
0: .* bp in .* sequences
...
...
algo/tests/should-get-tests/chimera-fake-2.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -t 0 -g $VIDJIL_DIR/germline -2 $VIDJIL_D
IR/data
/chimera-fake.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -t 0 -g $VIDJIL_DIR/germline -2 $VIDJIL_D
ATA
/chimera-fake.fa
$ The KmerSegmenter segments the three chimera reads on PSEUDO_MAX12 germline (-2)
1:unexpected .* -> .* 3
...
...
algo/tests/should-get-tests/chimera-fake-D.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_D
IR/data
/chimera-fake-D.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_D
ATA
/chimera-fake-D.fa
$ The KmerSegmenter segments the chimera reads on PSEUDO_MAX12 germline (-2)
f1:unexpected .* -> .* 2
...
...
algo/tests/should-get-tests/chimera-fake-VJ-germlines-trim.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_D
IR/data
/chimera-fake-VJ-trim.g $VIDJIL_D
IR/data
/chimera-fake-VJ.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_D
ATA
/chimera-fake-VJ-trim.g $VIDJIL_D
ATA
/chimera-fake-VJ.fa
# Testing a custom (fake) .g with special parameters for the algorithm
$ The KmerSegmenter segments no read in Y because of the parameter
...
...
algo/tests/should-get-tests/chimera-fake-VJ-germlines.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_D
IR/data
/chimera-fake-VJ.g $VIDJIL_D
IR/data
/chimera-fake-VJ.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_D
ATA
/chimera-fake-VJ.g $VIDJIL_D
ATA
/chimera-fake-VJ.fa
# Testing a custom (fake) germlines.data
$ Report the species
...
...
algo/tests/should-get-tests/chimera-fake-VJ.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_D
IR/data
/chimera-fake-VJ.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_D
ATA
/chimera-fake-VJ.fa
$ The KmerSegmenter segments the five chimera reads on PSEUDO_MAX12 germline (-2)
1:unexpected .* -> .* 5
...
...
algo/tests/should-get-tests/chimera-fake-half.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 100 -A -t 0 -g $VIDJIL_DIR/germline -4 $VIDJIL_D
IR/data
/chimera-fake-half.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 100 -A -t 0 -g $VIDJIL_DIR/germline -4 $VIDJIL_D
ATA
/chimera-fake-half.fa
# TODO: a more precise modeling should give a e-value computation that could make this work even with -e 1
$ The KmerSegmenter segments the six chimera reads on PSEUDO_MAX1U germline (-4)
...
...
algo/tests/should-get-tests/chimera-fake.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_D
IR/data
/chimera-fake.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_D
ATA
/chimera-fake.fa
$ Do not segment on any germline, even incomplete
1:junction detected in 0 reads
...
...
algo/tests/should-get-tests/chimera.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -uU -g $VIDJIL_DIR/germline $VIDJIL_D
IR/data
/chimera-trg.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -uU -g $VIDJIL_DIR/germline $VIDJIL_D
ATA
/chimera-trg.fa
$ Do not segment on IGL by chance
f1:IGL .* -> .* 0
...
...
algo/tests/should-get-tests/clones_lec.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -c clones -A -3 $VIDJIL_D
IR/data
/segment_lec.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -c clones -A -3 $VIDJIL_D
ATA
/segment_lec.fa
$ Extract 50bp windows (TRG)
1:found . 50-windows
...
...
algo/tests/should-get-tests/clones_simul.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 1 -r 1 $VIDJIL_D
IR/data
/clones_simul.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 1 -r 1 $VIDJIL_D
ATA
/clones_simul.fa
$ Junction extractions
1:found 25 50-windows in 66 reads
...
...
algo/tests/should-get-tests/clones_simul_cluster.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 0 -r 1 -n 5 $VIDJIL_D
IR/data
/clones_simul.fa ; cat out/clones_simul.vidjil
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 0 -r 1 -n 5 $VIDJIL_D
ATA
/clones_simul.fa ; cat out/clones_simul.vidjil
$ Window extractions
2:found 25 50-windows in 66 reads
...
...
algo/tests/should-get-tests/common-V-D.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -KA -z 0 -s \\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\# -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa $VIDJIL_D
IR/data
/common-V-D.fa ; cat out/common-V-D.affects
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -KA -z 0 -s \\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\# -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa $VIDJIL_D
ATA
/common-V-D.fa ; cat out/common-V-D.affects
$ Segments the sequence
1: SEG .* -> .* 1
...
...
algo/tests/should-get-tests/example_mouse.should-get
View file @
880abf7d
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -c segment -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_D
IR/data
/example_mouse.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -c segment -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_D
ATA
/example_mouse.fa
$ Segment sequence on IGK
1:segIGK.*IGKV.*IGKJ
...
...
Prev
1
2
3
4
Next
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment